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Trowel specifications

Information


Unique identifier OMICS_01111
Name Trowel
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux
Programming languages C++, Java
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Detlef Weigel

Publication for Trowel

Trowel citations

 (4)
library_books

Alignment free sequence comparison: benefits, applications, and tools

2017
Genome Biol
PMCID: 5627421
PMID: 28974235
DOI: 10.1186/s13059-017-1319-7

[…] eated to correct sequencing reads (e.g., Quorum []), designed mainly to be fast and memory efficient (e.g., Lighter [] using sampling of k-mers instead of counting), as well as highly accurate (e.g., Trowel [] using quality threshold rather than coverage cut-off in order to extract trusted k-mers).The advent of third-generation sequencing technologies (PacBio and Oxford Nanopore) provides an oppor […]

library_books

Evaluation of the impact of Illumina error correction tools on de novo genome assembly

2017
BMC Bioinformatics
PMCID: 5563063
PMID: 28821237
DOI: 10.1186/s12859-017-1784-8

[…] ference. We found that SPAdes and DISCOVAR consistently produced higher quality contigs than Velvet and IDBA. We were unable to produce assemblies with DISCOVAR using the reads that were corrected by Trowel and Fiona. Therefore, only SPAdes assemblies are discussed in detail in the remainder of this section.Table shows the contig and scaffold NGA50 values for all eight datasets and EC tools. For […]

library_books

A comparative study of k spectrum based error correction methods for next generation sequencing data analysis

2016
Hum Genomics
PMCID: 4965716
PMID: 27461106
DOI: 10.1186/s40246-016-0068-0

[…] eral well-regarded programs: HiTEC, SHREC, Coral, Quake, Reptile, DecGPU, and SGA []. Here, we also demonstrated that Musket yielded better performance metrics than Reptile. When authors of Bless [], Trowel [], and Lighter [] performed their comparative evaluations, they claimed that their own tools slightly outperformed Musket. However, if looking more specifically into simulated datasets, Musket […]

library_books

Denoising DNA deep sequencing data—high throughput sequencing errors and their correction

2015
Brief Bioinform
PMCID: 4719071
PMID: 26026159
DOI: 10.1093/bib/bbv029

[…] usion threshold), but creates its k-mer trust threshold for correction for each read separately. In this way, it adapts it to the local coverage and allows for k-mer coverage variations between reads.Trowel [] does not use a coverage threshold for its k-mer spectrum at all. Instead, it initially includes only k-mers whose bases all have quality values within the top 8% of the data set in at least […]

Citations

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Trowel institution(s)
Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
Trowel funding source(s)
This work was supported by the Max Planck Society.

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